Elbow Plot for Clustering
Heatmap
Cluster Enrichments
Ectoderm Cluster
## Uploading data to Enrichr... Done.
## Querying KEGG_2019... Done.
## Querying GO_Biological_Process_2018... Done.
## Parsing results... Done.
GO_Biological_Process_2018
KEGG_2019
Neuroectoderm Cluster
## Uploading data to Enrichr... Done.
## Querying KEGG_2019... Done.
## Querying GO_Biological_Process_2018... Done.
## Parsing results... Done.
GO_Biological_Process_2018
KEGG_2019
Mesoderm Cluster
## Uploading data to Enrichr... Done.
## Querying KEGG_2019... Done.
## Querying GO_Biological_Process_2018... Done.
## Parsing results... Done.
GO_Biological_Process_2018
KEGG_2019
Overlap between targets downregulated in WT vs. LOF and all clusters
Venn Diagram
Upset Plot
Resampling
Mesoderm
n
## [1] 50000
sum(res > 739)/n
## [1] 0
Neuroectoderm
n
## [1] 50000
sum(res > 292)/n
## [1] 0
Ectoderm
n
## [1] 50000
sum(res > 161)/n
## [1] 1
Overlap Enrichments
Downregulated & Neuroectoderm Overlap
## Uploading data to Enrichr... Done.
## Querying KEGG_2019... Done.
## Querying GO_Biological_Process_2018... Done.
## Parsing results... Done.
Downregulated & Mesoderm Overlap
## Uploading data to Enrichr... Done.
## Querying KEGG_2019... Done.
## Querying GO_Biological_Process_2018... Done.
## Parsing results... Done.
Mesoderm only
## Uploading data to Enrichr... Done.
## Querying KEGG_2019... Done.
## Querying GO_Biological_Process_2018... Done.
## Parsing results... Done.
Neuroectoderm only
## Uploading data to Enrichr... Done.
## Querying KEGG_2019... Done.
## Querying GO_Biological_Process_2018... Done.
## Parsing results... Done.
Downregulated only
## Uploading data to Enrichr... Done.
## Querying KEGG_2019... Done.
## Querying GO_Biological_Process_2018... Done.
## Parsing results... Done.
Overlap between targets UPREGULATED in WT vs. LOF and all clusters
Venn Diagram
Upset Plot
Resampling
Mesoderm
n
## [1] 50000
sum(res > 223)/n
## [1] 1
Neuroectoderm
n
## [1] 50000
sum(res > 109)/n
## [1] 0.99942
Ectoderm
n
## [1] 50000
sum(res > 629)/n
## [1] 0
Overlap Enrichments
Upregulated & Ectoderm Overlap
## Uploading data to Enrichr... Done.
## Querying KEGG_2019... Done.
## Querying GO_Biological_Process_2018... Done.
## Parsing results... Done.
Ectoderm only
## Uploading data to Enrichr... Done.
## Querying KEGG_2019... Done.
## Querying GO_Biological_Process_2018... Done.
## Parsing results... Done.
Upregulated only
## Uploading data to Enrichr... Done.
## Querying KEGG_2019... Done.
## Querying GO_Biological_Process_2018... Done.
## Parsing results... Done.
Combined Upset Plot
Session Info
## R version 4.0.5 (2021-03-31)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Big Sur 10.16
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] grid parallel stats4 stats graphics grDevices utils
## [8] datasets methods base
##
## other attached packages:
## [1] png_0.1-7 UpSetR_1.4.0
## [3] enrichR_3.0 VennDiagram_1.6.20
## [5] futile.logger_1.4.3 org.Dm.eg.db_3.12.0
## [7] msigdbr_7.2.1 cowplot_1.1.1
## [9] ggpubr_0.4.0 data.table_1.14.0
## [11] DT_0.17 forcats_0.5.1
## [13] dplyr_1.0.5 purrr_0.3.4
## [15] readr_1.4.0 tidyr_1.1.3
## [17] tibble_3.1.0 tidyverse_1.3.0
## [19] factoextra_1.0.7 ggplot2_3.3.3
## [21] cluster_2.1.1 stringr_1.4.0
## [23] enrichplot_1.13.0 ReactomePA_1.34.0
## [25] clusterProfiler_3.18.1 BSgenome.Dmelanogaster.UCSC.dm6_1.4.1
## [27] BSgenome_1.58.0 rtracklayer_1.50.0
## [29] Biostrings_2.58.0 XVector_0.30.0
## [31] pheatmap_1.0.12 geneplotter_1.68.0
## [33] annotate_1.68.0 XML_3.99-0.6
## [35] reshape_0.8.8 lattice_0.20-41
## [37] gridExtra_2.3 RColorBrewer_1.1-2
## [39] GenomicFeatures_1.42.3 AnnotationDbi_1.52.0
## [41] knitr_1.31 DESeq2_1.30.1
## [43] SummarizedExperiment_1.20.0 Biobase_2.50.0
## [45] MatrixGenerics_1.2.1 matrixStats_0.58.0
## [47] GenomicRanges_1.42.0 GenomeInfoDb_1.26.7
## [49] IRanges_2.24.1 S4Vectors_0.28.1
## [51] BiocGenerics_0.36.0
##
## loaded via a namespace (and not attached):
## [1] utf8_1.2.1 tidyselect_1.1.0 RSQLite_2.2.6
## [4] htmlwidgets_1.5.3 BiocParallel_1.24.1 scatterpie_0.1.5
## [7] munsell_0.5.0 withr_2.4.1 colorspace_2.0-0
## [10] GOSemSim_2.16.1 highr_0.8 rstudioapi_0.13
## [13] ggsignif_0.6.1 DOSE_3.16.0 labeling_0.4.2
## [16] GenomeInfoDbData_1.2.4 polyclip_1.10-0 bit64_4.0.5
## [19] farver_2.1.0 rprojroot_2.0.2 downloader_0.4
## [22] vctrs_0.3.7 treeio_1.14.4 generics_0.1.0
## [25] lambda.r_1.2.4 xfun_0.22 BiocFileCache_1.14.0
## [28] R6_2.5.0 graphlayouts_0.7.1 locfit_1.5-9.4
## [31] bitops_1.0-6 cachem_1.0.4 fgsea_1.16.0
## [34] DelayedArray_0.16.3 assertthat_0.2.1 scales_1.1.1
## [37] ggraph_2.0.5 gtable_0.3.0 tidygraph_1.2.0
## [40] rlang_0.4.10 genefilter_1.72.1 splines_4.0.5
## [43] rstatix_0.7.0 lazyeval_0.2.2 broom_0.7.6
## [46] checkmate_2.0.0 abind_1.4-5 BiocManager_1.30.12
## [49] yaml_2.2.1 reshape2_1.4.4 modelr_0.1.8
## [52] crosstalk_1.1.1 backports_1.2.1 qvalue_2.22.0
## [55] tools_4.0.5 ellipsis_0.3.1 jquerylib_0.1.3
## [58] Rcpp_1.0.6 plyr_1.8.6 progress_1.2.2
## [61] zlibbioc_1.36.0 RCurl_1.98-1.3 prettyunits_1.1.1
## [64] openssl_1.4.3 viridis_0.5.1 haven_2.3.1
## [67] ggrepel_0.9.1 fs_1.5.0 magrittr_2.0.1
## [70] futile.options_1.0.1 openxlsx_4.2.3 DO.db_2.9
## [73] reprex_2.0.0 reactome.db_1.74.0 hms_1.0.0
## [76] patchwork_1.1.1 evaluate_0.14 xtable_1.8-4
## [79] rio_0.5.26 readxl_1.3.1 compiler_4.0.5
## [82] biomaRt_2.46.3 crayon_1.4.1 shadowtext_0.0.7
## [85] htmltools_0.5.1.1 aplot_0.0.6 lubridate_1.7.10
## [88] DBI_1.1.1 formatR_1.8 tweenr_1.0.2
## [91] dbplyr_2.1.1 MASS_7.3-53.1 rappdirs_0.3.3
## [94] car_3.0-10 Matrix_1.3-2 cli_2.4.0
## [97] igraph_1.2.6 pkgconfig_2.0.3 rvcheck_0.1.8
## [100] GenomicAlignments_1.26.0 foreign_0.8-81 xml2_1.3.2
## [103] ggtree_2.4.2 bslib_0.2.4 rvest_1.0.0
## [106] digest_0.6.27 graph_1.68.0 rmarkdown_2.7
## [109] cellranger_1.1.0 fastmatch_1.1-0 tidytree_0.3.4
## [112] curl_4.3 Rsamtools_2.6.0 graphite_1.36.0
## [115] rjson_0.2.20 lifecycle_1.0.0 nlme_3.1-152
## [118] jsonlite_1.7.2 carData_3.0-4 viridisLite_0.4.0
## [121] askpass_1.1 fansi_0.4.2 pillar_1.6.0
## [124] fastmap_1.1.0 httr_1.4.2 survival_3.2-10
## [127] GO.db_3.12.1 glue_1.4.2 zip_2.1.1
## [130] bit_4.0.4 ggforce_0.3.3 stringi_1.5.3
## [133] sass_0.3.1 blob_1.2.1 memoise_2.0.0
## [136] ape_5.5